One of the frequent frustrations in molecular modeling workflows is not knowing what’s going on after launching a simulation. Whether you’re minimizing a system locally or in the cloud, staying updated on progress and accessing results efficiently can sometimes feel like guesswork.
If you’re using the GROMACS Wizard in SAMSON, there’s good news: it comes with a built-in job tracking system that makes managing local energy minimization jobs much more straightforward.
Launching a Minimization Job
Let’s assume you’ve prepared your system and are ready to run energy minimization locally. You click the “Minimize locally” button. Behind the scenes, SAMSON immediately spawns a GROMACS job using the executable provided either by default or a custom version you specified in the settings.
Now what?
This is where the Local Jobs interface becomes invaluable. As soon as a job is launched, it appears in the Local Jobs pane, accessible via the button highlighted below:
Why Monitor Local Jobs?
Here’s what you gain by using this feature:
- Real-time feedback: Know what stage the minimization is in, see if it’s still running or has completed.
- Error warnings: If something goes wrong (e.g. a bad input file or convergence issues), the job window will log it.
- Parallel workflow: You’re free to continue working inside SAMSON while the job runs in the background.
The ability to monitor jobs without leaving your modeling environment is especially helpful when managing multiple simulations or troubleshooting unexpected results.
What Happens When the Job Finishes?
Once energy minimization is complete and if only a single project is involved, a pop-up appears prompting you to import the results. You’ll be able to:
- Import the full trajectory or just the last frame
- Choose how to handle periodic boundary conditions
- Decide on centering options (e.g. center on the protein)
Not ready to import? No problem—you can cancel and the results will still be saved in the designated results folder (_em suffix), accessible whenever you’re ready.
The Human Side of Job Management
Many molecular modelers are familiar with either launching jobs through command-line GROMACS or using cumbersome GUI tools with less feedback. SAMSON’s approach gives a balance: a clean interface that keeps you informed, removes ambiguity, and reduces the mental overhead of managing simulations.
No more wondering “Did my simulation crash?” or guessing whether the minimization converged. With real-time tracking and structured imports, you get back control over your workflow with minimal friction.
To learn more, visit the full documentation on Energy Minimization with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.